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This project provides high-quality, chromosome-level reference genome assemblies for the tetraploid medicinal plant Panax ginseng and the diploid Panax vietnamensis var. vietnamensis. Utilizing a combination of long-read sequencing technologies (PacBio HiFi, Oxford Nanopore) and Hi-C scaffolding, we constructed complete pseudochromosomes to investigate the evolutionary relationships, synteny, and subgenome dynamics within the Panax genus. These genomic resources elucidate the allotetraploidization events in P. ginseng and serve as a valuable reference repository for comparative and functional genomics within the Araliaceae family.